August 01, 2013

3.4-7.9% Neandertal admixture in Eurasia ?

A new paper was posted on the arXiv.
UPDATE (Feb 18, 2014): This has now been published in Genetics.

arXiv:1307.8263 [q-bio.PE]

Maximum likelihood evidence for Neandertal admixture in Eurasian populations from three genomes

Konrad Lohse, Laurent A.F. Frantz

Although there has been much interest in estimating divergence and admixture from genomic data, it has proven difficult to distinguish gene flow after divergence from alternative histories involving structure in the ancestral population. The lack of a formal test to distinguish these scenarios has sparked recent controversy about the possibility of interbreeding between Neandertals and modern humans in Eurasia. We derive the probability of mutational configurations in non-recombining sequence blocks under alternative histories of divergence with admixture and ancestral structure. Dividing the genome into short blocks makes it possible to compute maximum likelihood estimates of parameters under both models. We apply this method to triplets of human Neandertal genomes and quantify the relative support for models of long-term population structure in the ancestral African popuation and admixture from Neandertals into Eurasian populations after their expansion out of Africa. Our analysis allows us -- for the first time -- to formally reject a history of ancestral population structure and instead reveals strong support for admixture from Neandertals into Eurasian populations at a higher rate (3.4%-7.9%) than suggested previously.

Moderate Neanderthal admixture of all Eurasians at more or less similar levels, and further moderate admixture of Melanesian and Aboriginal Australians, with some possible much smaller levels of admixture in a couple of African instances does not confirm that multi-regional hypothesis.

That hypothesis saw West-East Eurasian racial distinctions as rooted in archaic admixture, which is not true with the possible exception of an HLA complex of immune genes.

No, common ancestor is not a real possibility and has been long since ruled out.

http://johnhawks.net/taxonomy/term/1304

The only way a recent OoA ever worked is if you ignore/remove selection completely. If there's no selection and IF drift can account for the differences in races ie you are drifting in a direction instead of randomly scattering, this can be true. However those are two really big ifs.

Basically you have to believe what stephen jay gould does about evolution, which is psuedoscience paperback material. Anthropologists seem to have latched onto it but not biologists. Something like a sinus or appendix is not a quirk of random chance. It's way, way too complex for that, especially when you realize many sinuses grow only after birth in order to keep the head size small at birth, which has to be due to selection.

Recent OoA is basically saying that everyone formed in one place, but with all the current variations. Then by dumb luck and founder effects you got all people similar to each other in various areas. AND they stopped existing inside africa as well.

Andrew,I think that the proof of admixture destroys the primary tenet of OoA, that zero admixture occurred between the group labeled “modern” and pre-existing populations due to specific incompatibility. Once this primary plank is removed the rest pretty much crumbles away.

"I think that the proof of admixture destroys the primary tenet of OoA, that zero admixture occurred between the group labeled “modern” and pre-existing populations due to specific incompatibility."

I have never seen this stated in a scientific paper.

Conversely, the standard notion of multi-regionalism is that modern humans evolved separately on Earth over the past ~2 million years, with just some minor gene low. That notion is utterly incompatible with both autosomal and uniparental DNA, and also incompatible with any diligent fossil study.

Multi-regionalism is still dead, long lives ooA with some minor admixture.

"Conversely, the standard notion of multi-regionalism is that modern humans evolved separately on Earth over the past ~2 million years, with just some minor gene low. That notion is utterly incompatible with both autosomal and uniparental DNA, and also incompatible with any diligent fossil study."

I think you'd better have a look at the work of Robert G.Bednarik ( The origins of Human Modernity, in Humanities 2012, for example) and others. The main stream anglo-saxon way of thinking maybe is not the only possibility.

About the autosomal and uniparental DNA, a lot of unclear assumptions are made. In all the genetic papers, there is a lot of "estimating parameters", "ancestry estimation", " We approximate", " unknown west Eurasian population", " To account for sampling error, we simulated 40 individuals from the inferred ancestral west Eurasian population using the estimated allele frequencies". All this taken from the paper of Joseph K. Pickrell "Ancient west Eurasian ancestry in southern and eastern Africa".

Then you didn't read my comments in the last post. Don't know what OoA you are talking about but OoA completely attacks the idea of natural selection. That's why it's so popular.

I pointed out the idea of serial founder effect as the basis of all differences in people today.

"Conversely, the standard notion of multi-regionalism is that modern humans evolved separately on Earth over the past ~2 million years, with just some minor gene low. That notion is utterly incompatible with both autosomal and uniparental DNA, and also incompatible with any diligent fossil study."

Minor gene flow is really all it takes. Genes aren't mixing cakes, genes are about selection. If you wiped out all africa and repopulated it with finns then in a few thousand years the equatorial portions would be black again.

To me the fossil record says OoA is completely impossible.

300k-125k years ago we had brutish rhodiensis (some of the most brutish found in any period) skulls in africa, then then suddenly and possibly overlapping we had gracile modern man. Obviously didn't come from africa. Dieneke made a similar observation about a 100k year old skull in NA.

Anything interesting in africa is right along the border of the middle east. When connects right up to eurasia.

Plus neanderthals had much larger brains than anything in africa. Plus peking man is much more gracile than anything in africa. Plus ME and asia have been largely completely ignored until now and finds that apparently predate anything in africa are poo pooed and locked away without even dating them.

Not only is recent OoA false but I won't be surprised if there was never any OoA of any kind. There's also no evidence of what we think of as black people in africa until very recently. I don't even think they have been there very long but migrated out from asia just like the austronesians.

Like many critics of MRE you are conflating the widely discredited views of Coon with the theory posited by Wolpoff and Thorne. In my opinion the death of MRE has been widely exaggerated. In my opinion admixture is not something that can be qualified by terms such as major or minor. Admixture has either occurred or it has not. Until relatively recently the consensus was that it had not occurred. I have lost track of the many times I have read that Neandertals were a separate species, incapable of interbreeding with “modern” humans, in both scientific and popular literature.

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